This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The origin of spliceosomal introns has been in contention ever since they were first discovered. The ubiquity of introns in eukaryotes, their importance for RNA processing, as well as their role in disease make their origin and evolution a fundamental issue in biology. While there are many unanswered questions, there is a general consensus that group II introns are the most likely precursors. However, it is not known whether degeneration of group II introns is an ongoing process that can lead to the formation of novel spliceosomal introns, or has only occurred a limited number of times in the distant past. Based on diversity of group II introns and the frequent observation of putatively non-functional introns, degeneration is thought to be frequent. However, this process has rarely been studied in detail. The proposed project will study group II intron degeneration using three complementary approaches. First, publically available sequence data will be utilized to develop a global model of the group II intron life cycle. This will include the use of several search strategies to gain a complete picture of group II intron composition in bacterial and organellar genomes. The introns will be characterized using phylogenetic and sequence analyses and then fit into a model describing intron origin, degeneration, and loss. Next, the model will be refined using phylogenetic methods to understand the evolutionary relationship of the group II-intron encoded ORF and RNA structures. This method will first be used to determine whether the ORF and RNA have strictly coevolved and then to examine common degeneration patterns in secondary structure. Finally, an exemplar intron in red algae will be studied to better understand the pattern and temporal components of degeneration. In summary, the proposed project ranges in scope from broad-scale genomic analyses to a narrow focus on a single exemplar intron. The combination of approaches is expected to provide a more complete understanding of group II intron degeneration.